Warning: LOC list - is empty
wangyangXie opened this issue · 8 comments
2024年 07月 19日 星期五 14:36:11 CST Dependency checking:
All passed!
A custom library /public/home/xiewangyang/database/TE_db/sine_line_base.fa is provided via --curatedlib. Please make sure this is a manually curated library but not machine generated.
2024年 07月 19日 星期五 14:36:45 CST Obtain raw TE libraries using various structure-based programs:
2024年 07月 19日 星期五 14:36:45 CST EDTA_raw: Check dependencies, prepare working directories.
2024年 07月 19日 星期五 14:36:55 CST Start to find LTR candidates.
2024年 07月 19日 星期五 14:36:55 CST Identify LTR retrotransposon candidates from scratch.
Invalid value for shared scalar at /public/home/xiewangyang/software/miniconda3/envs/TE/share/LTR_retriever/bin/LTR.identifier.pl line 114, line 6072.
cp: 无法获取'D.odori.Chr.20240714.fasta.mod.retriever.scn.adj' 的文件状态(stat): 没有那个文件或目录
awk: 致命错误：cannot open file `D.odori.Chr.20240714.fasta.mod.pass.list' for reading: 没有那个文件或目录
Warning: LOC list - is empty.
Ive got the same issue, any solution?
Ive got the same issue, any solution?
Hasn't solved the problem yet.
May I ask how did you install EDTA?
Sorry for the late reply. Currently Conda install have some problems, would you like to try:
git clone https://github.com/oushujun/EDTA.git
mamba create -n EDTA2.2 -c conda-forge -c bioconda -c r annosine2 biopython blast cd-hit coreutils genericrepeatfinder genometools-genometools glob2 h5py==3.9 keras==2.11 ltr_finder ltr_retriever mdust multiprocess muscle openjdk pandas perl perl-text-soundex pyarrow python r-base r-dplyr regex repeatmodeler r-ggplot2 r-here r-tidyr scikit-learn swifter tensorflow==2.11 tesorter
This installation method might work better.
Sorry for the late reply. Currently Conda install have some problems, would you like to try: git clone https://github.com/oushujun/EDTA.git mamba create -n EDTA2.2 -c conda-forge -c bioconda -c r annosine2 biopython blast cd-hit coreutils genericrepeatfinder genometools-genometools glob2 h5py==3.9 keras==2.11 ltr_finder ltr_retriever mdust multiprocess muscle openjdk pandas perl perl-text-soundex pyarrow python r-base r-dplyr regex repeatmodeler r-ggplot2 r-here r-tidyr scikit-learn swifter tensorflow==2.11 tesorter
This installation method might work better.
Hi I used this recommended commands for installation of EDTA, however, its show errors bellow. Thanks in advance.
EDTA_raw.pl --genome $sample.chr.fa --species others --type tir --threads $th --overwrite 1
Fri Aug 9 20:51:55 CST 2024 EDTA_raw: Check dependencies, prepare working directories.
Fri Aug 9 20:52:18 CST 2024 Start to find TIR candidates.
Fri Aug 9 20:52:18 CST 2024 Identify TIR candidates from scratch.
Species: others
/work/home/miniforge3/envs/EDTA/bin/gt tirvish: error: fopen(): cannot open file 'TIR-Learner-+-gt_index.prj': No such file or directory
Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.fa: No such file or directory at /work/home/softwares/edta/EDTA/util/rename_tirlearner.pl line 19.
Warning: LOC list AE.H2.chr.fa.mod.TIR.ext30.list is empty.
Error: Error while loading sequence
Filter sequence based on TEsorter classifications. Unclassified sequences will also be output to the clean file.
Usage: perl cleanup_misclas.pl sequence.fa.rexdb.cls.tsv
Author: Shujun Ou (shujun.ou.1@gmail.com) 10/11/2019
mv: cannot stat 'AE.H2.chr.fa.mod.TIR.ext30.fa.pass.fa.dusted.cln.cln': No such file or directory
cp: cannot stat 'AE.H2.chr.fa.mod.TIR.ext30.fa.pass.fa.dusted.cln.cln.list': No such file or directory
cp: cannot stat 'AE.H2.chr.fa.mod.TIR.intact.raw.fa.anno.list': No such file or directory
Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.gff3: No such file or directory.
Warning: The TIR result file has 0 bp!
Fri Aug 9 20:56:17 CST 2024 Execution of EDTA_raw.pl is finished!
any updates ? did you add the EDTA folder to path ?